[
Methods Mol Biol,
2011]
Quantitative proteomics aims to identify and quantify proteins in cells or organisms that have been obtained from different biological origin (e.g., "healthy vs. diseased"), that have received different treatments, or that have different genetic backgrounds. Protein expression levels can be quantified by labeling proteins with stable isotopes, followed by mass spectrometric analysis. Stable isotopes can be introduced in vitro by reacting proteins or peptides with isotope-coded reagents (e.g., iTRAQ, reductive methylation). A preferred way, however, is the metabolic incorporation of heavy isotopes into cells or organisms by providing the label, in the form of amino acids (such as in SILAC) or salts, in the growth media. The advantage of in vivo labeling is that it does not suffer from side reactions or incomplete labeling that might occur in chemical derivatization. In addition, metabolic labeling occurs at the earliest possible moment in the sample preparation process, thereby minimizing the error in quantitation. Labeling with the heavy stable isotope of nitrogen (i.e., (15)N) provides an efficient way for accurate protein quantitation. Where the application of SILAC is mostly restricted to cell culture, (15)N labeling can be used for micro-organisms as well as a number of higher (multicellular) organisms. The most prominent examples of the latter are Caenorhabditis elegans and Drosophila (fruit fly), two important model organisms for a range of regulatory processes underlying developmental biology. Here we describe in detail the labeling with (15)N atoms, with a particular focus on fruit flies and C. elegans. We also describe methods for the identification and quantitation of (15)N-labeled proteins by mass spectrometry and bioinformatic analysis.
[
1987]
The concept of developmentally programmed senescence has been outlined by Leonard Hayflick (this volume), and examples from development have been used as exemplars of "developmentally programmed senescence" (Richard Russell, this volume). Unlike development, senescence has probably evolved in the absence of direct selection for increased longevity, perhaps as a direct result of the absence of such selection. (For an excellent review see Charlesworth.) A popular evolutionary model that has received experimental support suggests that senescence may result from pleiotropic effects of selection for adaptive life history characteristics. In the literature on aging, less rigorous arguements have been used to suggest that in human evolution, a delay in the age of senescence has been indirectly selected for by means of so-called longevity assurance or longevity-determinant genes. However, all explanations for the evolution of senescence are theoretical, and, with few exceptions, remain largely untested. Like Dr. Hayflick and Russell, I will assume that by developmental programming we mean genetic specification. I will use a general definition so as not to preclude examples that fail to meet one or more of the rigid criteria defined by Russell (this volume). This less rigid definition of programmed aging is necessary, because unlike development, where genetics has been successfully applied for 50 years, examples of genetic specification of senescent processes are quite few. In the literature on aging, it is still not widely accepted that mutants can alter fundamental patterns of senescent events in well-defined ways. One purpose of this presentation is to outline a few examples. In senescence, large batteries of new genes are not differentially regulated; this is quite unlike development, where many genes are differentially regulated. The molecular etiology of senescence is unknown in almost every instance and, as such, makes the study of aging a fascinating area for inquiry. If senescence is unlike development in lacking differential gene regulation, what are the approaches that are likely to yield useful results in the analysis of senescence and the aging process? The developmental genetic paradigm is a useful, indeed essential, theoretical construct for approaching the aging process in an experimental context. The lack of a suitable model organism in which classical and molecular genetics can be productively combined with other experimental techniques has impeded our understanding of senescence. Despite a general lack of evidence for genetic specification, there are instances where genetic specification is clearly evident; the analysis of mutational events that alter normal senescence in well-defined ways demonstrates this point. These instances also provide experimental models for dissecting the aging